Tag: Tool

Farsight 0.4.4 – Quantitative Tools for Studying Complex and Dynamic Biological Microenvironments from 4D/5D Microscopy Data

Farsight 0.4.4

:: DESCRIPTION

The goal of the FARSIGHT project is to develop and disseminate a next-generation toolkit of image analysis methods to enable quantitative studies of complex & dynamic tissue microenvironments that are imaged by modern optical microscopes. Examples of such microenvironments include brain tissue, stem cell niches, developing embryonic tissue, immune system components, and tumors. Progress in mapping these microenvironments is much too slow compared to the need. Our knowledge of these systems has been painstakingly “pieced together” from large numbers of fixed, 2-D images of specimens revealing a small fraction of the molecular ‘players’ involved. The goal of this project is to help accelerate progress by: (i) harnessing the power of modern microscopy to help see the microenvironments in a much more detailed, direct, and comprehensive manner; and (ii) computational tools to analyze the multi-dimensional data produced by these microscopes.

::DEVELOPER

Farsight Team

:: SCREENSHOTS

Farsight

:: REQUIREMENTS

  • Windows / MacOSX /Linux

:: DOWNLOAD

 Farsight

:: MORE INFORMATION

Citaition

The FARSIGHT trace editor: an open source tool for 3-D inspection and efficient pattern analysis aided editing of automated neuronal reconstructions.
Luisi J, Narayanaswamy A, Galbreath Z, Roysam B.
Neuroinformatics. 2011 Sep;9(2-3):305-15. doi: 10.1007/s12021-011-9115-0.

CUPSAT – Protein Stability Analysis Tool

CUPSAT

:: DESCRIPTION

CUPSAT (Cologne University Protein Stability Analysis Tool) is a tool to predict changes in protein stability upon point mutations. The prediction model uses amino acid-atom potentials and torsion angle distribution to assess the amino acid environment of the mutation site. Additionally, the prediction model can distinguish the amino acid environment using its solvent accessibility and secondary structure specificity.

::DEVELOPER

CUPSAT Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Parthiban V, Gromiha MM and Schomburg D. (2006)
CUPSAT: prediction of protein stability upon point mutations.
Nucleic Acids Research, 34, W239-42.

refolding 0.1 – Tools for Protein Unfolding and Refolding under the AFM

refolding 0.1

:: DESCRIPTION

refolding is a software that can drive and analyse mechanical refolding experiments when used with the commercial AFM setup ‘Picoforce AFM’, Bruker (previously Digital Instruments). We expect the software to be easily adaptable to other AFM setups.

::DEVELOPER

Daniel Aioanei (aioaneid@gmail.com), Marco Brucale and Bruno Samorí

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Java

:: DOWNLOAD

 refolding

:: MORE INFORMATION

Citation

D. Aioanei, M. Brucale, B. Samorì,
Open source platform for the execution and analysis of mechanical refolding experiments,
Bioinformatics (2011) 27 (3): 423-425.

Qeseq 0.2.2 – multipurpose ChIP-seq Analysis tool

Qeseq 0.2.2

:: DESCRIPTION

Qeseq is an algorithm to detect regions of increased ChIP read density relative to background. Qeseq employs critical novel elements, such as iterative recalibration and neighbor joining of reads to identify enriched regions of any length.

::DEVELOPER

Kluger Lab.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / MacOsX

:: DOWNLOAD

 Qeseq

:: MORE INFORMATION

Citation

Mariann Micsinai et al.
Picking ChIP-seq peak detectors for analyzing chromatin modification experiments
Nucl. Acids Res. (2012) 40 (9): e70.

Mugsy 1.2.3 – Multiple Whole Genome Alignment tool

Mugsy 1.2.3

:: DESCRIPTION

Mugsy is a multiple whole genome aligner. Mugsy uses Nucmer for pairwise alignment, a custom graph based segmentation procedure for identifying collinear regions, and the segment-based progressive multiple alignment strategy from Seqan::TCoffee. Mugsy accepts draft genomes in the form of multi-FASTA files and does not require a reference genome.

::DEVELOPER

Samuel V. Angiuoli ,  Dr. Steven Salzberg.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PErl

:: DOWNLOAD

 Mugsy

:: MORE INFORMATION

Citation

Angiuoli SV and Salzberg SL.
Mugsy: Fast multiple alignment of closely related whole genomes.
Bioinformatics 2011 27(3):334-4

PrimerMatch – PCR Primer Alignment Tools

PrimerMatch

:: DESCRIPTION

The Primer Match suite of tools is designed to find and count exact and near exact matches of short oligonucleotide sequences in large genomic databases. All matches to the oligos will be output, the tools guarantee a complete enumeration of all matches consistent with the search options. Substitutions, insertions and deletions can be prohibited in the start, end, 5′ or 3′ bases of oligos. Many options for constraining acceptable alignments and input/output formats are provided. The tools automatically optimize the sequence search strategies to match the search parameters.

::DEVELOPER

Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 PrimerMatch

:: MORE INFORMATION

XHM – Cross-hybridization tool

XHM

:: DESCRIPTION

XHM (cross hybridization on microarrays) is a tool for assessment of the reliability of hybridization signals by detecting potential cross-hybridizations on DNA microarrays.

::DEVELOPER

Uni Computing

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

XHM: a system for detection of potential cross hybridizations in DNA microarrays.
Flikka K, Yadetie F, Laegreid A, Jonassen I.
BMC Bioinformatics. 2004 Aug 27;5:117.

GRAST 1.0 – Genome Reduction Analysing Software Tool

GRAST 1.0

:: DESCRIPTION

GRAST allows the user to analyse genome reduction by whole genome comparison between a reduced genome and a reference genome (a close relative to the reduced genome). A number of the options in GRAST can also be used for a whole genome comparison of non-reduced genomes.

::DEVELOPER

Dr Mario Fares 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Perl

:: DOWNLOAD

 GRAST

:: MORE INFORMATION

Citation

GRAST: a new way of genome reduction analysis using comparative genomics.
Toft C, Fares MA.
Bioinformatics. 2006 Jul 1;22(13):1551-61. Epub 2006 Apr 6.

Tool for Biomedical Image Processing & Detection of Cancer using ANN

Biomedical Image Processing & Detection of Cancer

:: DESCRIPTION

 An automatic tool for prediction and classification of cancerous/non-cancerous squamosal cells using image processing and artificial neural networks (ANN). The ANN program is much more flexible and user friendly. It also optimizes number of hidden nodes itself based on the prediction accuracy. The neural network used here is a two layer neural networks and it uses standard back propagation algorithm. The first layer is use for detection of nucleus, cytoplasm and background of the image.Whereas the second layer is used to classify images into cancerous or non-cancerous based on three cellular features: size of nucleus, size of cytoplasm and ratio of nucleus/cytoplasm sizes. Using image processing techniques we extracted 15 features for selected pixel (using a mouse event program written in DOT NET framework) of an image over its 3×3 neighbouring matrix (using program written in MATLAB and C). These parameters are input to first layer of ANN.

::DEVELOPER

Project Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • Matlab

:: DOWNLOAD

 Project

:: MORE INFORMATION